Hidden instabilities are features that indirectly stabilize the target structure by destabilizing misfolded structures. These instabilities are usually only revealed when base pairs in the target structure are broken. In some cases, placing hidden instabilities in your design may increase its energy. This is not problematic so long as the energy of misfolded structures is increased to even greater extent.
Example #1[]
In the example to the right, a GU pair between nucleotides 2 and 78 creates a hidden instability. If the pair between bases 1 and 80 were broken, the resulting external loop would be unstable.
The use of a GU pair in this position actually increases the energy of the sequence folded into the target structure. It is most destabilizing, however, to undesired structures.
Example #2[]
In the second example, a hidden instability is used to stabilize a tricky isolated base pair between nucleotides 41 and 64. If the 48-55 pair is GC, energy can be lowered by breaking the 41-64 pair. This trick works for two reasons.
First, multiloops suffer an energy penalty when they contain AU or GU closing pairs.
Second, the UU terminal mismatch is stabilizing when it occurs in an internal loop, but destabilizing when it occurs in a multiloop. The loop containing the 48-55 pair is technically an internal loop. Breaking the 48-55 pair turns it into a multiloop. Another use of this trick is described in the GetSat post on catalyst points.